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Call for Exploratory Research Proposals, FY 2024



Decision notices

*Updated: June 20, 2023

Proposals must employ one or more of the capabilities highlighted below to advance scientific understanding in the Environmental Molecular Sciences Laboratory’s (EMSL’s) three Science Areas. As a guide, at least 30% of the research effort should focus on the highlighted capabilities in terms of requested hours or samples analyzed. Other EMSL Instruments and Resources may be used to supplement your research plan. Interested users are encouraged to work closely with EMSL scientists when developing the letter of intent (LOI) and subsequent proposal.

An LOI is required before submitting a proposal, and full proposals may only be submitted by invitation. EMSL utilizes dual anonymous peer review for this call. Full proposals must be anonymized to enable dual anonymous peer review. Successful proposals will include well-described research plans that can be completed within the nine-month project period.


For questions about the proposal submission process, please contact User Program Services.

For technical help with the EMSL User Portal (NEXUS), please contact NEXUS Support.

For scientific questions, contact EMSL staff identified in highlighted capabilities of the proposal call.

Highlighted Capabilities

  • Single-cell biology capabilities that encompass microscopy, activity-based probing, proteomics, and/or transcriptomics workflows to elucidate intercellular signaling, communication, and ensuing heterogeneity that underpin the phenotypes of microbial systems. (Contact: Alex Beliaev)  
  • Cell-free expression for structural biology, pathway engineering, and/or biochemical analyses that contribute to functional annotation, especially of proteins that are highly conserved across the fungal kingdom. (Contact: Scott Lea, James Evans)
    • The 1000 Fungal Proteins project aims to utilize structural biology resources, both experimental and computational, to accelerate the annotation of proteins of unknown function that are highly conserved across the fungal kingdom. User samples can enter the pipeline at various points, including users who already have proteins or metabolites highly purified and available for shipment, to those users who only have a gene sequence and would utilize our computational or experimental workflows from gene to structure.
  • Experiments focused on stable isotope labeling using multi-omics to study the flux of carbon or other nutrients through natural systems (e.g., soils, biofilms, axenic cultures) as well as to inform biotechnology applications. (Contact: Mary Lipton, David Hoyt)
  • Activity-based probes to explore enzyme function and characterize biochemical pathways. For example, EMSL recently developed a probe library to broadly profile amidase activity, which targets both canonical (peptide-like) and non-canonical amide hydrolase activity. We seek proposals utilizing this library or working with us to develop probes for other activities. (Contact: Sankar Krishnamoorthy
  • Artificial intelligence/machine learning methods to mine information from 2D chemical maps, process multimodal data, help co-register spatial data from different instruments, or expand 2D chemical info to 3D space. Proposals testing artificial intelligence/machine learning aided methods for molecular simulations are also encouraged. (Contact: Satish Karra)
  • Exploratory and statistical data analysis using one or more tools in the Multi-omics Analysis Portal (MAP) to analyze existing data. The MAP is a web-based portal with a suite of applications that provides users access to visualization and statistical techniques without requiring statistical programming. Data supported include metabolomics from nuclear magnetic resonance and liquid or gas chromatography mass spectrometry (LC-MS/GC-MS), isobaric labeled or unlabeled proteomics, LC-MS lipidomics, Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS), and RNA-Seq count data. (Contact: Kelly Stratton)
  • Measurements of the spatiotemporal distribution of roots and root exudates, metabolites, and essential elements in the rhizosphere, including C migration across soil–root–microbe interfaces, using any of the following capabilities:
    • 2D chemical mapping using mass spectrometry methods: matrix-assisted laser desorption/ionization mass spectrometry, nanospray desorption electrospray ionization mass spectrometry, or nanoscale secondary ion mass spectrometry (Contact: Amir Ahkami).
    • TerraForms (formerly synthetic soil habitats), such as rhizosphere-on-a-chip (Contact: Arunima Bhattacharjee, Jayde Aufrecht), integrated with one of the chemical mapping methods highlighted in this call.
    • Laser ablation-isotope ratio mass spectrometry (Contact: Sophie Lehmann).
    • X-ray computed tomography (XCT) integrated with 2D chemical mapping and artificial-intelligence-based data analysis (Contact: Tamas Varga).
    • 2D chemical mapping using scanning electron microscopy with energy-dispersive spectrometry (Contact: Odeta Qafoku).
  • Investigations of (1) emissions and atmospheric processing of volatile organic compounds and particles from biomass burning and plants, or (2) experimental-model studies of aerosol reactivity and particle nucleation, using any of the following capabilities:
  • Measurements of soil organic matter reactivity using pyrolysis gas chromatography mass spectroscopy (Contact: Qian Zhao), LC-FTICR-MS for improved formula assignment and expanded mass ranges (Contact: Will Kew, Nicole DiDonato), or FTICR-MS measurements coupled with mineral pool extractions and XCT or 2D imaging (Contact: Tamas Varga).
  • Imaging soil organic matter using at least one of the following methods: helium-ion microscopy (Contact: Shuttha Shutthanandan), transmission electron microscopy of microbial cells (Contact: Alice Dohnalkova), scanning electron microscopy with energy-dispersive spectrometry chemical analysis (Contact: Odeta Qafoku), atom probe tomography (Contact: Mark Wirth), and/or nanoscale secondary ion mass spectrometry (Contact: Jeremy Bougoure, John Cliff).

Review criteria

User proposals are peer reviewed against the four criteria listed below. For each criterion, the reviewer rates the proposal as Outstanding, Excellent, Good, Fundamentally Sound, or Questionable Impact as well as provides detailed comments on the quality of the proposal to support each rating, noting specifically the proposal's strengths and weaknesses. The reviewer also provides overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to EMSL management.

Criterion 1: Scientific merit and quality of the proposed research (50%)

Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity? If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)?

Criterion 2: Relevance of the proposed research to EMSL's mission (20%)

EMSL’s mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges.

EMSL supports the mission of the BER program in the DOE to achieve a predictive understanding of complex biological, Earth, and environmental systems for energy and infrastructure security, independence, and prosperity. BER seeks to understand the biological, biogeochemical, and physical processes that span from molecular and genomics-controlled scales to the regional and global scales that govern changes in watershed dynamics, climate, and the Earth system.

Starting with the genetic information encoded in organisms’ genomes, BER research seeks to discover the principles that guide the translation of the genetic code into the functional proteins and the metabolic and regulatory networks underlying the systems biology of plants and microbes as they respond to and modify their environments. This predictive understanding will enable design and reengineering of microbes and plants underpinning energy independence and a broad clean energy portfolio, including improved biofuels and bioproducts, improved carbon storage capabilities, and controlled biological transformation of materials such as nutrients and contaminants in the environment.

BER research further advances the fundamental understanding of the dynamic, physical, and biogeochemical processes required to systematically develop Earth system models that integrate across the atmosphere, land masses, oceans, sea ice, and subsurface. These predictive tools and approaches are needed to inform policies and plans for ensuring the security and resilience of the Nation’s critical infrastructure and natural resources.

Note: Projects with direct relevance in these areas will have the best chance for selection. Other projects of scientific significance are also welcomed, but the applicant should clearly outline how the project will further a DOE mission or other areas with economic or societal impact.

Potential Considerations: What is the relationship of the proposed research to EMSL's mission? Does the research project significantly advance the mission goals? How well does the project plan represent a unique or innovative application or development of EMSL capabilities?

Criterion 3: Impact of the proposed research on one or more EMSL Science Areas (20%)

Potential Considerations: Will the proposed research advance scientific and/or technological understanding of issues pertaining to one or more EMSL Science Areas? To what extent does the proposed research suggest and explore creative and original concepts related to one or more EMSL Science Areas? How strongly does it relate to the Science Area's focused topics as outlined in the most recent Call for Proposals? How well will it advance EMSL along the directions specifically outlined in the focused topics?

Criterion 4: Appropriateness and reasonableness of the request for EMSL resources for the proposed research (10%)

Potential Considerations: Are EMSL capabilities and resources essential to performing this research? Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity and/or scope of effort justify the duration of the proposed project—including any modifications to EMSL equipment to carry out research? Is the specified work plan practical and achievable for the proposed research project? Is the amount of time requested for each piece of equipment clearly justified and appropriate?